6QUQ

Crystal structure of glutathionylated glycolytic glyceraldehyde-3- phosphate dehydrogenase from Arabidopsis thaliana (AtGAPC1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.993 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates.

Zaffagnini, M.Marchand, C.H.Malferrari, M.Murail, S.Bonacchi, S.Genovese, D.Montalti, M.Venturoli, G.Falini, G.Baaden, M.Lemaire, S.D.Fermani, S.Trost, P.

(2019) Proc.Natl.Acad.Sci.USA 116: 26057-26065

  • DOI: 10.1073/pnas.1914484116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein aggregation is a complex physiological process, primarily determined by stress-related factors revealing the hidden aggregation propensity of proteins that otherwise are fully soluble. Here we report a mechanism by which glycolytic glyceralde ...

    Protein aggregation is a complex physiological process, primarily determined by stress-related factors revealing the hidden aggregation propensity of proteins that otherwise are fully soluble. Here we report a mechanism by which glycolytic glyceraldehyde-3-phosphate dehydrogenase of Arabidopsis thaliana (AtGAPC1) is primed to form insoluble aggregates by the glutathionylation of its catalytic cysteine (Cys149). Following a lag phase, glutathionylated AtGAPC1 initiates a self-aggregation process resulting in the formation of branched chains of globular particles made of partially misfolded and totally inactive proteins. GSH molecules within AtGAPC1 active sites are suggested to provide the initial destabilizing signal. The following removal of glutathione by the formation of an intramolecular disulfide bond between Cys149 and Cys153 reinforces the aggregation process. Physiological reductases, thioredoxins and glutaredoxins, could not dissolve AtGAPC1 aggregates but could efficiently contrast their growth. Besides acting as a protective mechanism against overoxidation, S-glutathionylation of AtGAPC1 triggers an unexpected aggregation pathway with completely different and still unexplored physiological implications.


    Organizational Affiliation

    Laboratoire de Biochimie Théorique, Unités Propre de Recherche Centre National de la Recherche Scientifique, Université Paris Diderot, Sorbonne Paris Cité, 75005 Paris, France.,Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.,Interdepartmental Centre for Industrial Research Health Sciences & Technologies, University of Bologna, 40064 Bologna, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; mirko.zaffagnini3@unibo.it paolo.trost@unibo.it.,Department of Chemistry G. Ciamician, University of Bologna, 40126 Bologna, Italy.,Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, 75005 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
O, R
334Arabidopsis thalianaMutation(s): 0 
Gene Names: GAPC1 (GAPC, GAPDH)
EC: 1.2.1.12
Find proteins for P25858 (Arabidopsis thaliana)
Go to UniProtKB:  P25858
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
O, R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GSH
Query on GSH

Download SDF File 
Download CCD File 
O, R
GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
O, R
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.993 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.249 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 77.365α = 90.00
b = 77.365β = 90.00
c = 406.814γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
XDSdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ItalyFARB2012-University of Bologna

Revision History 

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Database references